/*=========================================================================
 *
 *  Copyright Insight Software Consortium
 *
 *  Licensed under the Apache License, Version 2.0 (the "License");
 *  you may not use this file except in compliance with the License.
 *  You may obtain a copy of the License at
 *
 *         http://www.apache.org/licenses/LICENSE-2.0.txt
 *
 *  Unless required by applicable law or agreed to in writing, software
 *  distributed under the License is distributed on an "AS IS" BASIS,
 *  WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
 *  See the License for the specific language governing permissions and
 *  limitations under the License.
 *
 *=========================================================================*/
#ifndef __itkTestingExtractSliceImageFilter_hxx
#define __itkTestingExtractSliceImageFilter_hxx

#include "itkTestingExtractSliceImageFilter.h"
#include "itkImageRegionIterator.h"
#include "itkObjectFactory.h"
#include "itkProgressReporter.h"

namespace itk
{
namespace Testing
{
/**
 *
 */
template <typename TInputImage, typename TOutputImage>
ExtractSliceImageFilter<TInputImage, TOutputImage>::ExtractSliceImageFilter()
  :
#ifdef ITKV3_COMPATIBILITY
  m_DirectionCollaspeStrategy(DIRECTIONCOLLAPSETOGUESS)
#else
  this->DynamicMultiThreadingOff(); // NEEDED FOR ITKv5 backwards compatibility
m_DirectionCollaspeStrategy(DIRECTIONCOLLAPSETOUNKOWN)
#endif
{
  this->DynamicMultiThreadingOff(); // NEEDED FOR ITKv5 backwards compatibility
}

/**
 *
 */
template <typename TInputImage, typename TOutputImage>
void
ExtractSliceImageFilter<TInputImage, TOutputImage>::PrintSelf(std::ostream & os, Indent indent) const
{
  Superclass::PrintSelf(os, indent);

  os << indent << "ExtractionRegion: " << m_ExtractionRegion << std::endl;
  os << indent << "OutputImageRegion: " << m_OutputImageRegion << std::endl;
  os << indent << "DirectionCollaspeStrategy: " << m_DirectionCollaspeStrategy << std::endl;
}

template <typename TInputImage, typename TOutputImage>
void
ExtractSliceImageFilter<TInputImage, TOutputImage>::CallCopyOutputRegionToInputRegion(
  InputImageRegionType &        destRegion,
  const OutputImageRegionType & srcRegion)
{
  ExtractSliceImageFilterRegionCopierType extractImageRegionCopier;

  extractImageRegionCopier(destRegion, srcRegion, m_ExtractionRegion);
}

template <typename TInputImage, typename TOutputImage>
void
ExtractSliceImageFilter<TInputImage, TOutputImage>::SetExtractionRegion(InputImageRegionType extractRegion)
{
  m_ExtractionRegion = extractRegion;

  unsigned int        nonzeroSizeCount = 0;
  InputImageSizeType  inputSize = extractRegion.GetSize();
  OutputImageSizeType outputSize;
  outputSize.Fill(0);
  OutputImageIndexType outputIndex;
  outputIndex.Fill(0);
  /**
   * check to see if the number of non-zero entries in the extraction region
   * matches the number of dimensions in the output image.
   */
  for (unsigned int i = 0; i < InputImageDimension; ++i)
  {
    if (inputSize[i])
    {
      outputSize[nonzeroSizeCount] = inputSize[i];
      outputIndex[nonzeroSizeCount] = extractRegion.GetIndex()[i];
      ++nonzeroSizeCount;
    }
  }

  if (nonzeroSizeCount != OutputImageDimension)
  {
    itkExceptionMacro("Extraction Region not consistent with output image");
  }

  m_OutputImageRegion.SetSize(outputSize);
  m_OutputImageRegion.SetIndex(outputIndex);
  this->Modified();
}

/**
 * ExtractSliceImageFilter can produce an image which is a different resolution
 * than its input image.  As such, ExtractSliceImageFilter needs to provide an
 * implementation for GenerateOutputInformation() in order to inform
 * the pipeline execution model.  The original documentation of this
 * method is below.
 *
 * \sa ProcessObject::GenerateOutputInformaton()
 */
template <typename TInputImage, typename TOutputImage>
void
ExtractSliceImageFilter<TInputImage, TOutputImage>::GenerateOutputInformation()
{
  // do not call the superclass' implementation of this method since
  // this filter allows the input and the output to be of different dimensions

  // get pointers to the input and output
  TOutputImage *      outputPtr = this->GetOutput();
  const TInputImage * inputPtr = this->GetInput();

  if (!outputPtr || !inputPtr)
  {
    return;
  }

  // Set the output image size to the same value as the extraction region.
  outputPtr->SetLargestPossibleRegion(m_OutputImageRegion);

  // Set the output spacing and origin
  const ImageBase<InputImageDimension> * phyData;

  phyData = dynamic_cast<const ImageBase<InputImageDimension> *>(this->GetInput());

  if (phyData)
  {
    // Copy what we can from the image from spacing and origin of the input
    // This logic needs to be augmented with logic that select which
    // dimensions to copy

    const typename InputImageType::SpacingType &   inputSpacing = inputPtr->GetSpacing();
    const typename InputImageType::DirectionType & inputDirection = inputPtr->GetDirection();
    const typename InputImageType::PointType &     inputOrigin = inputPtr->GetOrigin();

    typename OutputImageType::SpacingType   outputSpacing;
    typename OutputImageType::DirectionType outputDirection;
    typename OutputImageType::PointType     outputOrigin;
    outputOrigin.Fill(0.0);

    if (static_cast<unsigned int>(OutputImageDimension) > static_cast<unsigned int>(InputImageDimension))
    {
      // copy the input to the output and fill the rest of the
      // output with zeros.
      for (unsigned int i = 0; i < InputImageDimension; ++i)
      {
        outputSpacing[i] = inputSpacing[i];
        outputOrigin[i] = inputOrigin[i];
        for (unsigned int dim = 0; dim < InputImageDimension; ++dim)
        {
          outputDirection[i][dim] = inputDirection[i][dim];
        }
      }
      for (unsigned int i = InputImageDimension; i < OutputImageDimension; ++i)
      {
        outputSpacing[i] = 1.0;
        outputOrigin[i] = 0.0;
        for (unsigned int dim = 0; dim < InputImageDimension; ++dim)
        {
          outputDirection[i][dim] = 0.0;
        }
        outputDirection[i][i] = 1.0;
      }
    }
    else
    {
      // copy the non-collapsed part of the input spacing and origing to the
      // output
      outputDirection.SetIdentity();
      int nonZeroCount = 0;
      for (unsigned int i = 0; i < InputImageDimension; ++i)
      {
        if (m_ExtractionRegion.GetSize()[i])
        {
          outputSpacing[nonZeroCount] = inputSpacing[i];
          outputOrigin[nonZeroCount] = inputOrigin[i];
          int nonZeroCount2 = 0;
          for (unsigned int dim = 0; dim < InputImageDimension; ++dim)
          {
            if (m_ExtractionRegion.GetSize()[dim])
            {
              outputDirection[nonZeroCount][nonZeroCount2] = inputDirection[nonZeroCount][dim];
              ++nonZeroCount2;
            }
          }
          ++nonZeroCount;
        }
      }
    }

    // if the filter changes from a higher to a lower dimension, or
    // if, after rebuilding the direction cosines, there's a zero
    // length cosine vector, reset the directions to identity.
    switch (m_DirectionCollaspeStrategy)
    {
      case DIRECTIONCOLLAPSETOIDENTITY:
      {
        outputDirection.SetIdentity();
      }
      break;
      case DIRECTIONCOLLAPSETOSUBMATRIX:
      {
        if (vnl_determinant(outputDirection.GetVnlMatrix()) == 0.0)
        {
          itkExceptionMacro(<< "Invalid submatrix extracted for collapsed direction.");
        }
      }
      break;
      case DIRECTIONCOLLAPSETOGUESS:
      {
        if (vnl_determinant(outputDirection.GetVnlMatrix()) == 0.0)
        {
          outputDirection.SetIdentity();
        }
      }
      break;
      case DIRECTIONCOLLAPSETOUNKOWN:
      default:
      {
        itkExceptionMacro(<< "It is required that the strategy for collapsing"
                             " the direction matrix be explicitly specified. "
                             "Set with either myfilter->SetDirectionCollapseToIdentity()"
                             " or myfilter->SetDirectionCollapseToSubmatrix() "
                          << typeid(ImageBase<InputImageDimension> *).name());
      }
    }

    // set the spacing and origin
    outputPtr->SetSpacing(outputSpacing);
    outputPtr->SetDirection(outputDirection);
    outputPtr->SetOrigin(outputOrigin);
    outputPtr->SetNumberOfComponentsPerPixel(inputPtr->GetNumberOfComponentsPerPixel());
  }
  else
  {
    // pointer could not be cast back down
    itkExceptionMacro(<< "itk::ExtractSliceImageFilter::GenerateOutputInformation "
                      << "cannot cast input to " << typeid(ImageBase<InputImageDimension> *).name());
  }
}

/**
 * ExtractSliceImageFilter can be implemented as a multithreaded filter.
 * Therefore, this implementation provides a ThreadedGenerateData()
 * routine which is called for each processing thread. The output
 * image data is allocated automatically by the superclass prior to
 * calling ThreadedGenerateData().  ThreadedGenerateData can only
 * write to the portion of the output image specified by the
 * parameter "outputRegionForThread"
 *
 */
template <typename TInputImage, typename TOutputImage>
void
ExtractSliceImageFilter<TInputImage, TOutputImage>::ThreadedGenerateData(
  const OutputImageRegionType & outputRegionForThread,
  ThreadIdType                  threadId)
{
  itkDebugMacro(<< "Actually executing");

  // Get the input and output pointers
  const TInputImage * inputPtr = this->GetInput();
  TOutputImage *      outputPtr = this->GetOutput();

  // support progress methods/callbacks
  ProgressReporter progress(this, threadId, outputRegionForThread.GetNumberOfPixels());

  // Define the portion of the input to walk for this thread
  InputImageRegionType inputRegionForThread;
  this->CallCopyOutputRegionToInputRegion(inputRegionForThread, outputRegionForThread);

  // Define the iterators.
  using OutputIterator = ImageRegionIterator<TOutputImage>;
  using InputIterator = ImageRegionConstIterator<TInputImage>;

  OutputIterator outIt(outputPtr, outputRegionForThread);
  InputIterator  inIt(inputPtr, inputRegionForThread);

  // walk the output region, and sample the input image
  while (!outIt.IsAtEnd())
  {
    // copy the input pixel to the output
    outIt.Set(static_cast<OutputImagePixelType>(inIt.Get()));
    ++outIt;
    ++inIt;
    progress.CompletedPixel();
  }
}

/**
 *
 */
template <typename TInputImage, typename TOutputImage>
void
ExtractSliceImageFilter<TInputImage, TOutputImage>::SetInput(const TInputImage * input)
{
  // Process object is not const-correct so the const_cast is required here
  this->ProcessObject::SetNthInput(0, const_cast<TInputImage *>(input));
}

/**
 *
 */
template <typename TInputImage, typename TOutputImage>
const TInputImage *
ExtractSliceImageFilter<TInputImage, TOutputImage>::GetInput(void) const
{
  if (this->GetNumberOfInputs() < 1)
  {
    return 0;
  }

  return static_cast<const TInputImage *>(this->ProcessObject::GetInput(0));
}
} // end namespace Testing
} // end namespace itk

#endif
